Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

xhemi
by Joost Janssen 06 Mar '24

06 Mar '24

External Email - Use Caution Dear Doug, The objective is to have _regional_ laterality index for thickness for aparc mapped to the left hemisphere. The following commands work without error but are they correct for meeting my objective? Thanks. surfreg --s $subject --t fsaverage_sym --lh --no-annot surfreg --s $subject --t fsaverage_sym --lh --no-annot --xhemi mri_convert $subject/surf/lh.thickness $subject/surf/lh.thickness.mgh mri_convert $subject/surf/rh.thickness $subject/surf/rh.thickness.mgh mris_apply_reg --src $subject/surf/lh.thickness.mgh --trg $subject/surf/lh.thickness.lh.fsaverage_sym.mgh --streg $subject/surf/lh.fsaverage_sym.sphere.reg fsaverage_sym/surf/lh.sphere.reg mris_apply_reg --src $subject/surf/rh.thickness.mgh --trg $subject/surf/rh.thickness.lh.fsaverage_sym.mgh --streg $subject/xhemi/surf/lh.fsaverage_sym.sphere.reg fsaverage_sym/surf/lh.sphere.reg fscalc $subject/surf/lh.thickness.lh.fsaverage_sym.mgh pctdiff0 $subject/surf/rh.thickness.lh.fsaverage_sym.mgh div 200 -o $subject/surf/li.thickness.lh.fsaverage_sym.mgh mri_segstats --annot fsaverage lh aparc --i $subject/surf/li.thickness.lh.fsaverage_sym.mgh --sum $subject/stats/li.thickness.aparc.stats -joost

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Hi
by Farzaneh, Hana 06 Mar '24

06 Mar '24

Hfarzaneh(a)mgh.harvard.edu Get Outlook for iOS<https://aka.ms/o0ukef>

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Spring 2024 FreeSurfer course
by Sennott, Liam Ricker 06 Mar '24

06 Mar '24

Hello all, The next virtual FreeSurfer course will be held on April 29th, 30th, and May 1st. Registration for this virtual FreeSurfer course is opening on Monday, March 11th at 12pm Eastern Daylight Time. Visit our course website to find out more information: https://surfer.nmr.mgh.harvard.edu/fswiki/VirtualCourse Specific questions about the course can be sent to fscourse(a)mgb.org<mailto:fscourse@mgb.org>

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remote access to freesurfer installation...
by Gonzalo Rojas Costa 06 Mar '24

06 Mar '24

External Email - Use Caution Hi: Is there a freesurfer facility where an MRI study can be processed remotely? Sincerely, Gonzalo Rojas Costa

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Unexpected skull shape after wraped to MNI
by GOFFINET Sara 06 Mar '24

06 Mar '24

External Email - Use Caution Hello, I ran freesurfer recon_all on a T1 MRI sequence (you can find the orig T1 in Screenshtot1) and my participant's brain warped to MNI (worig.nii) looks deformed (Screenshot2). Do you know why is there a bump (the worig file does not overlay well on MNI) while the reconstruction of the pial surface (lh.pial, rh.pial) shows no abnormality? Thanks in advance, Sara Goffinet

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TRACULA GLM output question
by Hoskinson, Kristen 05 Mar '24

05 Mar '24

External Email - Use Caution We’re working on a project where we ran 3 groups, 1 covariate, and ran a glm looking at white matter at cross-sections from TRACULA output, covarying for functional activation. We’re now wanting to plot out the interaction/slopes per group, but are having trouble locating the data that would allow that step. Could anyone direct us? Thank you! -- Kristen R. Hoskinson, Ph.D. (she/her) Associate Professor of Pediatrics The Ohio State University College of Medicine Principal Investigator, Social Cognition, Adjustment, and Neurodevelopment (SCAN) Lab Center for Biobehavioral Health The Abigail Wexner Research Institute at Nationwide Children's Hospital 700 Children's Drive Columbus, Ohio 43205 (614) 722-3021 kristen.hoskinson(a)nationwidechildrens.org<mailto:kristen.robinson@nationwidechildrens.org>

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Citing the bert dataset
by Shounak Nandi 05 Mar '24

05 Mar '24

External Email - Use Caution Hi, I have used the bert<https://secure-web.cisco.com/1iRXfF4vATaFfKjWoBFscMdP724sTiLA-ialN9LArN1Wnu…> <https://secure-web.cisco.com/1iRXfF4vATaFfKjWoBFscMdP724sTiLA-ialN9LArN1Wnu…> dataset in one of the scientific works and was curious how I cite it? I am eager to know your thoughts. Thanks, Shounak Nandi Radiology Trainee, Department of Radiology and Radiological Science, Division of Cancer Imaging Research, Johns Hopkins School of Medicine, Baltimore, MD

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2 PhD positions in layer-fMRI of high-level cognition at the Max Planck Institute for Biological Cybernetics in Tübingen , Germany
by Romy Lorenz 05 Mar '24

05 Mar '24

External Email - Use Caution The newly established Cognitive Neuroscience & Neurotechnology group led by Dr. Romy Lorenz is looking for two enthusiastic PhD students (m/f/d) to join our growing team at the Max Planck Institute for Biological Cybernetics in Tübingen, Germany. Our lab focuses on advancing our understanding of the frontoparietal brain network mechanisms that underpin high-level cognition and adaptive behaviour. For this, we pursue an interdisciplinary research programme that allows studying this brain system at multiple levels of granularity. Our methodology involves subject-specific brain-computer interface technology, fMRI at 3T and ultrahigh (i.e., 7T and 9.4T) magnetic field strengths (for resolving cortical layers), EEG, non-invasive brain stimulation as well as machine learning. You can find out more about our work at: https://secure-web.cisco.com/1DTFYMuBJpaThDmnsZx8BTzF2AVMPT_WTXTuNSPnfZdIr4… We are seeking two ambitious PhD students who will work on the exciting field of ultrahigh resolution fMRI that allows to investigate the human cortex at the scale of layers and columns. The ideal candidates should have a master’s degree in cognitive (neuro)science, psychology, computer science, biomedical or electrical engineering, physics, or related disciplines. A strong background in fMRI data analysis (e.g., FSL, Freesurfer, ANTS) and very good programming skills in Bash on Linux, Matlab and/or Python are required. Prior experience in MRI data acquisition and experience with ultrahigh resolution fMRI (e.g., at 7T) is desirable but not necessary. Equally, experience with machine learning-methods, code sharing platforms (e.g. GitHub) and high-performance computing clusters are highly desirable. The Max Planck Institute for Biological Cybernetics offers a world-leading research environment with access to the latest cutting-edge MRI hardware (including a Siemens 9.4T and Prisma 3T for humans as well as a 14.2T small animal system) and other excellent research facilities (EEG, eye-tracking, fMRI-TMS). The PhD student will receive generous support for professional travel and research needs (~2500€/year). Additionally, the student will have the opportunity to become part of the Graduate Training Centre of Neuroscience that provides training courses, summer schools and conferences to further educate doctoral students. Further, the Institute is part of the TübingenNeuroCampus (with more than 100 active groups), offering a vibrant community of international researchers and enriching environment of collaboration. The position is available from May 2024 on and remains open until filled. The salary is paid in accordance with the collective agreement for the public sector (65% TVL-E13, amounting to ~2000€ net per month). For more details about the two advertised PhD positions and how to apply, please see: https://secure-web.cisco.com/1HBQhEBJ4wZ9IS2zpkXMkuIwzjxkS5db6bDYMd0qWJKNhn… Dr. Romy Lorenz Max Planck Research Group Leader Research Group Cognitive Neuroscience & Neurotechnology Max Planck Institute for Biological Cybernetics Tübingen, Germany romy.lorenz(a)tuebingen.mpg.de http://secure-web.cisco.com/1-aUWpt7JdIbcqswpTsDWYsyChmNmUZeOBqxYreWQN848To…

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Assistance Request: Issue with Merging .mgh Files in Ubuntu18
by Rosie 05 Mar '24

05 Mar '24

External Email - Use Caution Dear Support Team, I'm reaching out for assistance with merging two .mgh files. As I try to generate a surface mapping for all subjects, I merged all volume files (.nii.gz) by mrcalc. So I get a volume file whose voxel value represents the number of valid subjects. And then I convert it to .mgh using mri_vol2surf. But the value of each voxel seems to be thrown out. Because I found the max value of .mgh is not the same as .nii file. I guess I should merge files of all subject in mgh format to maintain the number of valid subjects, but it seems to be a volume encoded surface file format. So I don't know how to merge them. I'm working on Ubuntu18. I would be very grateful for your assistance. Best, Rosie

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Re: [Freesurfer] recon-all-clinical synthseg error
by fsbuild 04 Mar '24

04 Mar '24

External Email - Use Caution  It could help to know what OS version and what Freesurfer version you are running.  From your path /usr/local/freesurfer it looks like you are running a Freesurfer release, e.g., 7.4.1. - R. On Feb 25, 2024, at 21:45, Agata Wolna <awolna(a)mit.edu> wrote:        External Email - Use Caution        Hi!I'm trying to run recon-all-clinical but I'm running into an error with the SynthSeg at the very beginning. Do you have any hints what the problem might be here? Here's the full error message:the following problem occured with image [mypath]/mri/native.mgz :Traceback (most recent call last):  File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 303, in predict    image, aff, h, im_res, shape, pad_idx, crop_idx = preprocess(path_image=path_images[i],  File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 554, in preprocess    im, _, aff, n_dims, n_channels, h, im_res = get_volume_info(path_image, True)  File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 1456, in get_volume_info    im, aff, header = load_volume(path_volume, im_only=False)  File "/usr/local/freesurfer/python/scripts/mri_synthseg", line 1377, in load_volume    x = nib.load(path_volume)  File "/usr/local/freesurfer/python/lib/python3..8/site-packages/nibabel/loadsave.py", line 110, in load    img = image_klass.from_filename(filename, **kwargs)  File "/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/dataobj_images.py", line 503, in from_filename    return klass.from_file_map(file_map, mmap=mmap, keep_file_open=keep_file_open)  File "/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/freesurfer/mghformat.py", line 526, in from_file_map    header = klass.header_class.from_fileobj(mghf)  File "/usr/local/freesurfer/python/lib/python3.8/site-packages/nibabel/freesurfer/mghformat.py", line 171, in from_fileobj    + int(klass._data_type_codes.bytespervox[tp]) * np.prod(hdr_str_to_np['dims'])KeyError: 10resuming program executionERROR: some problems occured for the following inputs (see corresponding errors above):[mypath]/mri/native.mgzError in SynthSegBest,Agata_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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